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Merge pull request #273 from EcoExtreML/add_Trap_to_BMI
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Redefine Evap and Trap arrays
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@MostafaGomaa93
MostafaGomaa93 authored Dec 17, 2024
2 parents 0f267e0 + b97137c commit 8d3ef75
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,9 +15,13 @@ The 1.6.1 release comes with minor changes as:
**Fixed:**
- The bug in the calculation of the soil type index discussed in
[#252](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/252)
- The EVAP is removed discussed in [#274](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/274) and fixed in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
- The shape of Evap variable is changed to match BMI requirements discussed in [#274](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/274) and fixed in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)

**Added:**
- The recharge index is exposed to BMI in [#257](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/257)
- The Trap variable (after changing its shape) is exposed to BMI discussed in [#271](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/271) and added in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
- The FullCSVfiles option is added in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)


<a name="1.6.0"></a>
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7 changes: 7 additions & 0 deletions docs/getting_started.md
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Expand Up @@ -76,6 +76,13 @@ EndTime=2001-01-02T00:00
InputPath=/path_to_model_input_folder/
OutputPath=/path_to_model_output_folder/
```
The configuration file could also contain the optional key `FullCSVfiles`. If
`FullCSVfiles=0`, the model will **not** store some **large** binary files in
csv format. The default value is `FullCSVfiles=1`. To know which files are
stored in csv format, see the function `bin_to_csv()` in `src/+io` folder.
```text
FullCSVfiles=0
```

See example configuration files below:

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Binary file modified run_model_on_snellius/exe/STEMMUS_SCOPE
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4 changes: 2 additions & 2 deletions src/+energy/calculateBoundaryConditions.m
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@@ -1,5 +1,5 @@
function [RHS, EnergyMatrices] = calculateBoundaryConditions(BoundaryCondition, EnergyMatrices, HBoundaryFlux, ForcingData, SoilVariables, ...
Precip, EVAP, Delt_t, r_a_SOIL, Rn_SOIL, RHS, L, KT, ModelSettings, GroundwaterSettings)
Precip, Evap, Delt_t, r_a_SOIL, Rn_SOIL, RHS, L, KT, ModelSettings, GroundwaterSettings)
%{
Determine the boundary condition for solving the energy equation, see
STEMMUS Technical Notes.
Expand Down Expand Up @@ -46,6 +46,6 @@
else
L_ts = L(n);
SH = 0.1200 * Constants.c_a * (SoilVariables.T(n) - ForcingData.Ta_msr(KT)) / r_a_SOIL(KT);
RHS(n) = RHS(n) + 100 * Rn_SOIL(KT) / 1800 - Constants.RHOL * L_ts * EVAP(KT) - SH + Constants.RHOL * Constants.c_L * (ForcingData.Ta_msr(KT) * Precip(KT) + BoundaryCondition.DSTOR0 * SoilVariables.T(n) / Delt_t); % J cm-2 s-1
RHS(n) = RHS(n) + 100 * Rn_SOIL(KT) / 1800 - Constants.RHOL * L_ts * Evap - SH + Constants.RHOL * Constants.c_L * (ForcingData.Ta_msr(KT) * Precip(KT) + BoundaryCondition.DSTOR0 * SoilVariables.T(n) / Delt_t); % J cm-2 s-1
end
end
3 changes: 1 addition & 2 deletions src/+init/defineInitialValues.m
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Expand Up @@ -178,8 +178,7 @@

%% Structure 5: variables with zeros(Nmsrmn / 10, 1)
fields = {
'Tp_t', 'Evap', 'Tbtm', 'r_a_SOIL', 'Rn_SOIL', 'EVAP', ...
'PSItot', 'sfactortot', 'Tsur'
'Tbtm', 'r_a_SOIL', 'Rn_SOIL', 'PSItot', 'sfactortot', 'Tsur'
};
structures{5} = helpers.createStructure(zeros(Dur_tot, 1), fields);

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147 changes: 77 additions & 70 deletions src/+io/bin_to_csv.m
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@@ -1,4 +1,4 @@
function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings, FullCSVfiles)
%% flu
flu_names = {'simulation_number', 'nu_iterations', 'year', 'DoY', ...
'Rntot', 'lEtot', 'Htot', ...
Expand Down Expand Up @@ -91,60 +91,6 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
Sim_qtot_units = repelem({'cm s-1'}, length(depth));
write_output(Sim_qtot_names, Sim_qtot_units, fnames.Sim_qtot_file, n_col.Sim_qtot, ns, true);

%% Spectrum (added on 19 September 2008)
spectrum_hemis_optical_names = {'hemispherically integrated radiation spectrum'};
spectrum_hemis_optical_units = {'W m-2 um-1'};
write_output(spectrum_hemis_optical_names, spectrum_hemis_optical_units, fnames.spectrum_hemis_optical_file, n_col.spectrum_hemis_optical, ns, true);

spectrum_obsdir_optical_names = {'radiance spectrum in observation direction'};
spectrum_obsdir_optical_units = {'W m-2 sr-1 um-1'};
write_output(spectrum_obsdir_optical_names, spectrum_obsdir_optical_units, fnames.spectrum_obsdir_optical_file, n_col.spectrum_obsdir_optical, ns, true);

if options.calc_ebal
write_output({'thermal BlackBody emission spectrum in observation direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_obsdir_BlackBody_file, n_col.spectrum_obsdir_BlackBody, ns, true);
if options.calc_planck
write_output({'thermal emission spectrum in hemispherical direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_hemis_thermal_file, n_col.spectrum_hemis_thermal, ns, true);
write_output({'thermal emission spectrum in observation direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_obsdir_thermal_file, n_col.spectrum_obsdir_thermal, ns, true);
end
end
write_output({'irradiance'}, {'W m-2 um-1'}, ...
fnames.irradiance_spectra_file, n_col.irradiance_spectra, ns, true);
write_output({'reflectance'}, {'fraction of radiation in observation direction *pi / irradiance'}, ...
fnames.reflectance_file, n_col.reflectance, ns, true);
%% input and parameter values (added June 2012)
% write_output(fnames.pars_and_input_file, true)
% write_output(fnames.pars_and_input_short_file, true)
%% Optional Output
if options.calc_vert_profiles
write_output({'Fraction leaves in the sun, fraction of observed, fraction of observed&visible per layer'}, {'rows: simulations or time steps, columns: layer numbers'}, ...
fnames.gap_file, n_col.gap, ns, true);
write_output({'aPAR per leaf layer'}, {'umol m-2 s-1'}, ...
fnames.layer_aPAR_file, n_col.layer_aPAR, ns, true);
write_output({'aPAR by Cab per leaf layer'}, {'umol m-2 s-1'}, ...
fnames.layer_aPAR_Cab_file, n_col.layer_aPAR_Cab, ns, true);
if options.calc_ebal
write_output({'leaf temperature of sunlit leaves, shaded leaves, and weighted average leaf temperature per layer'}, {'^oC ^oC ^oC'}, ...
fnames.leaftemp_file, n_col.leaftemp, ns, true);
write_output({'sensible heat flux per layer'}, {'W m-2'}, ...
fnames.layer_H_file, n_col.layer_H, ns, true);
write_output({'latent heat flux per layer'}, {'W m-2'}, ...
fnames.layer_LE_file, n_col.layer_LE, ns, true);
write_output({'photosynthesis per layer'}, {'umol m-2 s-1'}, ...
fnames.layer_A_file, n_col.layer_A, ns, true);
write_output({'average NPQ = 1-(fm-fo)/(fm0-fo0), per layer'}, {''}, ...
fnames.layer_NPQ_file, n_col.layer_NPQ, ns, true);
write_output({'net radiation per leaf layer'}, {'W m-2'}, ...
fnames.layer_Rn_file, n_col.layer_Rn, ns, true);
end
if options.calc_fluor
fluorescence_names = {'supward fluorescence per layer'};
fluorescence_units = {'W m-2'};
write_output(fluorescence_names, fluorescence_units, fnames.layer_fluorescence_file, n_col.layer_fluorescence, ns, true);
end
end
if options.calc_fluor
write_output({'fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_file, n_col.fluorescence, ns, true);
Expand All @@ -154,21 +100,83 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
write_output({'fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution, for PSII only'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescencePSII_file, n_col.fluorescencePSII, ns, true);
end
write_output({'hemispherically integrated fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_hemis_file, n_col.fluorescence_hemis, ns, true);
write_output({'total emitted fluorescence by all leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_emitted_by_all_leaves_file, n_col.fluorescence_emitted_by_all_leaves, ns, true);
write_output({'total emitted fluorescence by all photosystems for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_emitted_by_all_photosystems_file, n_col.fluorescence_emitted_by_all_photosystems, ns, true);
write_output({'TOC fluorescence contribution from sunlit leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_sunlit_file, n_col.fluorescence_sunlit, ns, true);
write_output({'TOC fluorescence contribution from shaded leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_shaded_file, n_col.fluorescence_shaded, ns, true);
write_output({'TOC fluorescence contribution from from leaves and soil after scattering for wavelenghts of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_scattered_file, n_col.fluorescence_scattered, ns, true);
end
write_output({'Bottom of canopy irradiance in the shaded fraction, and average BOC irradiance'}, {'First 2162 columns: shaded fraction. Last 2162 columns: average BOC irradiance. Unit: Wm-2 um-1'}, ...
fnames.BOC_irradiance_file, n_col.BOC_irradiance, ns, true);

% Optional for large output files
if FullCSVfiles
%% Spectrum (added on 19 September 2008)
spectrum_hemis_optical_names = {'hemispherically integrated radiation spectrum'};
spectrum_hemis_optical_units = {'W m-2 um-1'};
write_output(spectrum_hemis_optical_names, spectrum_hemis_optical_units, fnames.spectrum_hemis_optical_file, n_col.spectrum_hemis_optical, ns, true);

spectrum_obsdir_optical_names = {'radiance spectrum in observation direction'};
spectrum_obsdir_optical_units = {'W m-2 sr-1 um-1'};
write_output(spectrum_obsdir_optical_names, spectrum_obsdir_optical_units, fnames.spectrum_obsdir_optical_file, n_col.spectrum_obsdir_optical, ns, true);

if options.calc_ebal
write_output({'thermal BlackBody emission spectrum in observation direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_obsdir_BlackBody_file, n_col.spectrum_obsdir_BlackBody, ns, true);
if options.calc_planck
write_output({'thermal emission spectrum in hemispherical direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_hemis_thermal_file, n_col.spectrum_hemis_thermal, ns, true);
write_output({'thermal emission spectrum in observation direction'}, {'W m-2 sr-1 um-1'}, ...
fnames.spectrum_obsdir_thermal_file, n_col.spectrum_obsdir_thermal, ns, true);
end
end
write_output({'irradiance'}, {'W m-2 um-1'}, ...
fnames.irradiance_spectra_file, n_col.irradiance_spectra, ns, true);
write_output({'reflectance'}, {'fraction of radiation in observation direction *pi / irradiance'}, ...
fnames.reflectance_file, n_col.reflectance, ns, true);

%% input and parameter values (added June 2012)
% write_output(fnames.pars_and_input_file, true)
% write_output(fnames.pars_and_input_short_file, true)

%% Optional Output
if options.calc_vert_profiles
write_output({'Fraction leaves in the sun, fraction of observed, fraction of observed&visible per layer'}, {'rows: simulations or time steps, columns: layer numbers'}, ...
fnames.gap_file, n_col.gap, ns, true);
write_output({'aPAR per leaf layer'}, {'umol m-2 s-1'}, ...
fnames.layer_aPAR_file, n_col.layer_aPAR, ns, true);
write_output({'aPAR by Cab per leaf layer'}, {'umol m-2 s-1'}, ...
fnames.layer_aPAR_Cab_file, n_col.layer_aPAR_Cab, ns, true);
if options.calc_ebal
write_output({'leaf temperature of sunlit leaves, shaded leaves, and weighted average leaf temperature per layer'}, {'^oC ^oC ^oC'}, ...
fnames.leaftemp_file, n_col.leaftemp, ns, true);
write_output({'sensible heat flux per layer'}, {'W m-2'}, ...
fnames.layer_H_file, n_col.layer_H, ns, true);
write_output({'latent heat flux per layer'}, {'W m-2'}, ...
fnames.layer_LE_file, n_col.layer_LE, ns, true);
write_output({'photosynthesis per layer'}, {'umol m-2 s-1'}, ...
fnames.layer_A_file, n_col.layer_A, ns, true);
write_output({'average NPQ = 1-(fm-fo)/(fm0-fo0), per layer'}, {''}, ...
fnames.layer_NPQ_file, n_col.layer_NPQ, ns, true);
write_output({'net radiation per leaf layer'}, {'W m-2'}, ...
fnames.layer_Rn_file, n_col.layer_Rn, ns, true);
end
if options.calc_fluor
fluorescence_names = {'supward fluorescence per layer'};
fluorescence_units = {'W m-2'};
write_output(fluorescence_names, fluorescence_units, fnames.layer_fluorescence_file, n_col.layer_fluorescence, ns, true);
end
end
if options.calc_fluor
write_output({'hemispherically integrated fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_hemis_file, n_col.fluorescence_hemis, ns, true);
write_output({'total emitted fluorescence by all leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_emitted_by_all_leaves_file, n_col.fluorescence_emitted_by_all_leaves, ns, true);
write_output({'total emitted fluorescence by all photosystems for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_emitted_by_all_photosystems_file, n_col.fluorescence_emitted_by_all_photosystems, ns, true);
write_output({'TOC fluorescence contribution from sunlit leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_sunlit_file, n_col.fluorescence_sunlit, ns, true);
write_output({'TOC fluorescence contribution from shaded leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_shaded_file, n_col.fluorescence_shaded, ns, true);
write_output({'TOC fluorescence contribution from from leaves and soil after scattering for wavelenghts of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_scattered_file, n_col.fluorescence_scattered, ns, true);
end
write_output({'Bottom of canopy irradiance in the shaded fraction, and average BOC irradiance'}, {'First 2162 columns: shaded fraction. Last 2162 columns: average BOC irradiance. Unit: Wm-2 um-1'}, ...
fnames.BOC_irradiance_file, n_col.BOC_irradiance, ns, true);
end

fclose('all');

Expand All @@ -177,7 +185,6 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
for k = 1:numel(fn)
delete(fnames.(fn{k}));
end

end

function write_output(header, units, bin_path, f_n_col, ns, not_header)
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2 changes: 1 addition & 1 deletion src/+io/output_data_binary.m
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Expand Up @@ -10,7 +10,7 @@
%% Fluxes product
flu_out = [k iter.counter xyt.year(k) xyt.t(k) fluxes.Rntot fluxes.lEtot fluxes.Htot fluxes.Rnctot fluxes.lEctot, ...
fluxes.Hctot fluxes.Actot fluxes.Rnstot fluxes.lEstot fluxes.Hstot fluxes.Gtot fluxes.Resp 1E6 * fluxes.aPAR, ...
1E6 * fluxes.aPAR_Cab fluxes.aPAR / rad.PAR fluxes.aPAR_Wm2 1E6 * rad.PAR rad.Eoutf rad.Eoutf ./ fluxes.aPAR_Wm2 Trap(k) * 10 Evap(k) * 10 Trap(k) * 10 + Evap(k) * 10 fluxes.GPP fluxes.NEE];
1E6 * fluxes.aPAR_Cab fluxes.aPAR / rad.PAR fluxes.aPAR_Wm2 1E6 * rad.PAR rad.Eoutf rad.Eoutf ./ fluxes.aPAR_Wm2 Trap * 10 Evap * 10 Trap * 10 + Evap * 10 fluxes.GPP fluxes.NEE];
n_col.flu = length(flu_out);
fwrite(f.flu_file, flu_out, 'double');

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9 changes: 8 additions & 1 deletion src/+io/read_config.m
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@@ -1,4 +1,4 @@
function [InputPath, OutputPath, InitialConditionPath] = read_config(config_file)
function [InputPath, OutputPath, InitialConditionPath, FullCSVfiles] = read_config(config_file)

file_id = fopen(config_file);
config = textscan(file_id, '%s %s', 'HeaderLines', 0, 'Delimiter', '=');
Expand All @@ -17,3 +17,10 @@

indx = find(strcmp(config_vars, 'InitialConditionPath'));
InitialConditionPath = config_paths{indx};

indx = find(strcmp(config_vars, 'FullCSVfiles'));
if isempty(indx)
FullCSVfiles = 1;
else
FullCSVfiles = str2num(config_paths{indx});
end
2 changes: 1 addition & 1 deletion src/+soilmoisture/calculateBoundaryConditions.m
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Expand Up @@ -108,7 +108,7 @@
C4(n - 1, 2) = 0;
C4_a(n - 1) = 0;
else
RHS(n) = RHS(n) + AVAIL0 - Evap(KT);
RHS(n) = RHS(n) + AVAIL0 - Evap;
end
end
HeatMatrices.C4 = C4;
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17 changes: 6 additions & 11 deletions src/+soilmoisture/calculateEvapotranspiration.m
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@@ -1,4 +1,4 @@
function [Rn_SOIL, Evap, EVAP, Trap, r_a_SOIL, Srt, RWUs, RWUg] = calculateEvapotranspiration(InitialValues, ForcingData, SoilVariables, KT, RWU, fluxes, Srt, ModelSettings, GroundwaterSettings)
function [Rn_SOIL, Evap, Trap, r_a_SOIL, Srt, RWUs, RWUg] = calculateEvapotranspiration(InitialValues, ForcingData, SoilVariables, KT, RWU, fluxes, Srt, ModelSettings, GroundwaterSettings)

if ~GroundwaterSettings.GroundwaterCoupling % no Groundwater coupling, added by Mostafa
indxBotm = 1; % index of bottom layer is 1, STEMMUS calculates from bottom to top
Expand All @@ -14,22 +14,18 @@
U = 100 .* (ForcingData.WS_msr(KT));
AR = soilmoisture.calculateAerodynamicResistance(U);
r_a_SOIL = AR.soil;

Ta = ForcingData.Ta_msr(KT);
Evap = InitialValues.Evap;
EVAP = InitialValues.EVAP;

if fluxes.lEctot < 1000 && fluxes.lEstot < 800 && fluxes.lEctot > -300 && fluxes.lEstot > -300 && any(SoilVariables.TT > 5)
lambda1 = (2.501 - 0.002361 * Ta) * 1E6;
lambda2 = (2.501 - 0.002361 * SoilVariables.Tss(KT)) * 1E6;
Evap(KT) = fluxes.lEstot / lambda2 * 0.1; % transfer to second value unit: cm s-1
EVAP(KT, 1) = Evap(KT);
Tp_t = fluxes.lEctot / lambda1 * 0.1; % transfer to second value
Evap = fluxes.lEstot / lambda2 * 0.1; % transfer to second value unit: cm s-1
Trap = fluxes.lEctot / lambda1 * 0.1; % transfer to second value
Srt1 = RWU * 100 ./ ModelSettings.DeltZ';
else
Evap(KT) = 0; % transfer to second value unit: cm s-1
EVAP(KT, 1) = Evap(KT);
Tp_t = 0; % transfer to second value
Evap = 0; % transfer to second value unit: cm s-1
Trap = 0; % transfer to second value
RWU = 0 * RWU;
Srt1 = 0 ./ ModelSettings.DeltZ';
end

Expand All @@ -38,7 +34,6 @@
Srt(i, j) = Srt1(i, 1);
end
end
Trap(KT) = Tp_t; % root water uptake integration by ModelSettings.DeltZ;

% Calculate root water uptake from soil water (RWUs) and groundwater (RWUg)
RWU = RWU * 100; % unit conversion from m/sec to cm/sec
Expand Down
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